Job ID = 6454111 SRX = SRX183521 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:54:04 prefetch.2.10.7: 1) Downloading 'SRR567538'... 2020-06-21T08:54:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:56:41 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:56:42 prefetch.2.10.7: 'SRR567538' is valid 2020-06-21T08:56:42 prefetch.2.10.7: 1) 'SRR567538' was downloaded successfully Read 15120499 spots for SRR567538/SRR567538.sra Written 15120499 spots for SRR567538/SRR567538.sra 2020-06-21T08:57:34 prefetch.2.10.7: 1) Downloading 'SRR567539'... 2020-06-21T08:57:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:59:22 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:59:23 prefetch.2.10.7: 'SRR567539' is valid 2020-06-21T08:59:23 prefetch.2.10.7: 1) 'SRR567539' was downloaded successfully Read 17451185 spots for SRR567539/SRR567539.sra Written 17451185 spots for SRR567539/SRR567539.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:09 32571684 reads; of these: 32571684 (100.00%) were unpaired; of these: 27648523 (84.89%) aligned 0 times 3389067 (10.40%) aligned exactly 1 time 1534094 (4.71%) aligned >1 times 15.11% overall alignment rate Time searching: 00:04:10 Overall time: 00:04:10 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_rmdupse_core] 1409391 / 4923161 = 0.2863 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 18:06:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX183521/SRX183521.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX183521/SRX183521.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX183521/SRX183521.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX183521/SRX183521.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 18:06:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:06:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:06:24: 1000000 INFO @ Sun, 21 Jun 2020 18:06:29: 2000000 INFO @ Sun, 21 Jun 2020 18:06:35: 3000000 INFO @ Sun, 21 Jun 2020 18:06:38: #1 tag size is determined as 46 bps INFO @ Sun, 21 Jun 2020 18:06:38: #1 tag size = 46 INFO @ Sun, 21 Jun 2020 18:06:38: #1 total tags in treatment: 3513770 INFO @ Sun, 21 Jun 2020 18:06:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:06:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:06:38: #1 tags after filtering in treatment: 3513583 INFO @ Sun, 21 Jun 2020 18:06:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:06:38: #1 finished! INFO @ Sun, 21 Jun 2020 18:06:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:06:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:06:39: #2 number of paired peaks: 3138 INFO @ Sun, 21 Jun 2020 18:06:39: start model_add_line... INFO @ Sun, 21 Jun 2020 18:06:39: start X-correlation... INFO @ Sun, 21 Jun 2020 18:06:39: end of X-cor INFO @ Sun, 21 Jun 2020 18:06:39: #2 finished! INFO @ Sun, 21 Jun 2020 18:06:39: #2 predicted fragment length is 159 bps INFO @ Sun, 21 Jun 2020 18:06:39: #2 alternative fragment length(s) may be 159 bps INFO @ Sun, 21 Jun 2020 18:06:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX183521/SRX183521.05_model.r INFO @ Sun, 21 Jun 2020 18:06:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:06:39: #3 Pre-compute pvalue-qvalue table... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 18:06:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX183521/SRX183521.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX183521/SRX183521.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX183521/SRX183521.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX183521/SRX183521.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 18:06:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:06:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:06:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:06:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX183521/SRX183521.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:06:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX183521/SRX183521.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:06:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX183521/SRX183521.05_summits.bed INFO @ Sun, 21 Jun 2020 18:06:53: Done! INFO @ Sun, 21 Jun 2020 18:06:53: 1000000 pass1 - making usageList (397 chroms): 1 millis pass2 - checking and writing primary data (3071 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:06:59: 2000000 INFO @ Sun, 21 Jun 2020 18:07:04: 3000000 INFO @ Sun, 21 Jun 2020 18:07:07: #1 tag size is determined as 46 bps INFO @ Sun, 21 Jun 2020 18:07:07: #1 tag size = 46 INFO @ Sun, 21 Jun 2020 18:07:07: #1 total tags in treatment: 3513770 INFO @ Sun, 21 Jun 2020 18:07:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:07:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:07:08: #1 tags after filtering in treatment: 3513583 INFO @ Sun, 21 Jun 2020 18:07:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:07:08: #1 finished! INFO @ Sun, 21 Jun 2020 18:07:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:07:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:07:08: #2 number of paired peaks: 3138 INFO @ Sun, 21 Jun 2020 18:07:08: start model_add_line... INFO @ Sun, 21 Jun 2020 18:07:08: start X-correlation... INFO @ Sun, 21 Jun 2020 18:07:08: end of X-cor INFO @ Sun, 21 Jun 2020 18:07:08: #2 finished! INFO @ Sun, 21 Jun 2020 18:07:08: #2 predicted fragment length is 159 bps INFO @ Sun, 21 Jun 2020 18:07:08: #2 alternative fragment length(s) may be 159 bps INFO @ Sun, 21 Jun 2020 18:07:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX183521/SRX183521.10_model.r INFO @ Sun, 21 Jun 2020 18:07:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:07:08: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sun, 21 Jun 2020 18:07:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX183521/SRX183521.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX183521/SRX183521.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX183521/SRX183521.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX183521/SRX183521.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sun, 21 Jun 2020 18:07:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:07:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:07:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:07:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX183521/SRX183521.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:07:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX183521/SRX183521.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:07:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX183521/SRX183521.10_summits.bed INFO @ Sun, 21 Jun 2020 18:07:23: Done! INFO @ Sun, 21 Jun 2020 18:07:23: 1000000 pass1 - making usageList (197 chroms): 2 millis pass2 - checking and writing primary data (2092 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:07:29: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:07:34: 3000000 INFO @ Sun, 21 Jun 2020 18:07:37: #1 tag size is determined as 46 bps INFO @ Sun, 21 Jun 2020 18:07:37: #1 tag size = 46 INFO @ Sun, 21 Jun 2020 18:07:37: #1 total tags in treatment: 3513770 INFO @ Sun, 21 Jun 2020 18:07:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:07:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:07:38: #1 tags after filtering in treatment: 3513583 INFO @ Sun, 21 Jun 2020 18:07:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:07:38: #1 finished! INFO @ Sun, 21 Jun 2020 18:07:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:07:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:07:38: #2 number of paired peaks: 3138 INFO @ Sun, 21 Jun 2020 18:07:38: start model_add_line... INFO @ Sun, 21 Jun 2020 18:07:38: start X-correlation... INFO @ Sun, 21 Jun 2020 18:07:38: end of X-cor INFO @ Sun, 21 Jun 2020 18:07:38: #2 finished! INFO @ Sun, 21 Jun 2020 18:07:38: #2 predicted fragment length is 159 bps INFO @ Sun, 21 Jun 2020 18:07:38: #2 alternative fragment length(s) may be 159 bps INFO @ Sun, 21 Jun 2020 18:07:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX183521/SRX183521.20_model.r INFO @ Sun, 21 Jun 2020 18:07:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:07:38: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:07:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:07:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX183521/SRX183521.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:07:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX183521/SRX183521.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:07:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX183521/SRX183521.20_summits.bed INFO @ Sun, 21 Jun 2020 18:07:53: Done! pass1 - making usageList (107 chroms): 2 millis pass2 - checking and writing primary data (1409 records, 4 fields): 7 millis CompletedMACS2peakCalling